[med-svn] [spades] 02/07: Merge tag 'upstream/3.7.0+dfsg'
Sascha Steinbiss
sascha at steinbiss.name
Wed Feb 24 22:08:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository spades.
commit 7fb6cc59f328d65c62b6aa79502d8d4d7ea29a30
Merge: 6abd0e2 5546f51
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Wed Feb 24 19:19:03 2016 +0000
Merge tag 'upstream/3.7.0+dfsg'
Upstream version 3.7.0+dfsg
LICENSE | 16 +-
README | 14 +-
VERSION | 2 +-
changelog.html | 8 +
configs/corrector/corrector.info | 7 +
.../debruijn/{config.info.template => config.info} | 23 +-
configs/debruijn/config.info.template | 23 +-
configs/debruijn/construction.info | 23 +
...sed_rr.info.template => coverage_based_rr.info} | 0
configs/debruijn/detail_info_printer.info | 43 +
configs/debruijn/detail_info_printer.info.template | 47 +-
configs/debruijn/distance_estimation.info | 91 ++
.../{log.properties.template => log.properties} | 8 +
configs/debruijn/log.properties.template | 8 +
configs/debruijn/path_extend/pe_params.info | 186 +++
.../debruijn/path_extend/pe_params.info.template | 257 ++--
configs/debruijn/simplification.info | 561 ++++++++
configs/debruijn/simplification.info.template | 647 +++++----
configs/debruijn/tsa.info | 5 +
configs/dipspades/config.info | 64 +
.../log.properties} | 26 +-
.../hammer/{config.info.template => config.info} | 4 +-
configs/hammer/config.info.template | 4 +-
configs/ionhammer/ionhammer.cfg | 12 +
dipspades.py | 14 +-
dipspades_manual.html | 6 +
ext/include/city/city.h | 109 ++
ext/include/city/citycrc.h | 43 +
ext/include/llvm/AlignOf.h | 189 +++
ext/include/llvm/PointerEmbeddedInt.h | 87 ++
ext/include/llvm/PointerIntPair.h | 192 +++
ext/include/llvm/PointerLikeTypeTraits.h | 92 ++
ext/include/llvm/PointerSumType.h | 176 +++
ext/src/CMakeLists.txt | 3 +-
ext/src/ConsensusCore/Version.cpp | 2 +-
{src/mph_index => ext/src/cityhash}/CMakeLists.txt | 8 +-
ext/src/cityhash/city.cc | 639 +++++++++
ext/src/ssw/ssw.c | 349 ++---
ext/src/ssw/ssw_cpp.cpp | 258 ++--
manual.html | 151 ++-
spades.py | 21 +-
spades_init.py | 2 +-
src/CMakeLists.txt | 7 +-
src/cmake/pack.cmake | 6 +-
src/corrector/CMakeLists.txt | 14 +-
src/corrector/contig_processor.cpp | 132 +-
src/corrector/contig_processor.hpp | 14 +-
src/corrector/dataset_processor.cpp | 4 +-
src/corrector/dataset_processor.hpp | 3 +-
src/corrector/interesting_pos_processor.hpp | 2 +-
src/corrector/main.cpp | 4 +-
src/corrector/read.cpp | 164 ---
src/debruijn/CMakeLists.txt | 15 +-
src/debruijn/bwa_pair_info_filler.cpp | 407 ++++++
src/debruijn/bwa_pair_info_filler.hpp | 254 ++++
src/debruijn/config_struct.cpp | 169 ++-
src/debruijn/config_struct.hpp | 66 +-
src/debruijn/construction.cpp | 4 +-
src/debruijn/dataset_readers.hpp | 12 +-
src/debruijn/debruijn_data.hpp | 15 +-
src/debruijn/debruijn_stats.cpp | 1050 +++++++--------
src/debruijn/detail_coverage.hpp | 3 +
src/debruijn/distance_estimation.cpp | 14 +-
src/debruijn/early_simplification.hpp | 52 +-
src/debruijn/gap_closer.cpp | 58 +-
src/debruijn/genome_consistance_checker.cpp | 236 ++++
src/debruijn/genome_consistance_checker.hpp | 126 +-
src/debruijn/genome_storage.cpp | 45 +
src/debruijn/genome_storage.hpp | 33 +
src/debruijn/genomic_info_filler.cpp | 6 +-
src/debruijn/genomic_quality.hpp | 5 +
src/debruijn/graph_pack.hpp | 19 +-
src/debruijn/graph_simplification.hpp | 1000 --------------
src/debruijn/graphio.hpp | 75 +-
src/debruijn/indices/edge_multi_index.hpp | 1 +
src/debruijn/indices/kmer_extension_index.hpp | 1 -
src/debruijn/indices/kmer_splitters.hpp | 8 +-
src/debruijn/indices/perfect_hash_map.hpp | 6 +
src/debruijn/is_counter.hpp | 153 +--
src/debruijn/kmer_coverage_model.cpp | 2 +-
src/debruijn/launch.hpp | 36 +-
src/debruijn/long_read_mapper.hpp | 67 +-
src/debruijn/main.cpp | 1 +
src/debruijn/mismatch_correction.cpp | 7 +-
src/debruijn/overlap_analysis.hpp | 113 ++
src/debruijn/pacbio/pac_index.hpp | 71 +-
src/debruijn/pacbio/pacbio_gap_closer.hpp | 50 +-
src/debruijn/pacbio_aligning.cpp | 54 +-
src/debruijn/pair_info_count.cpp | 71 +-
src/debruijn/pair_info_filler.hpp | 43 +-
src/debruijn/pair_info_improver.hpp | 210 +--
src/debruijn/paired_statistics.hpp | 4 +-
src/debruijn/path_extend/bidirectional_path.hpp | 136 +-
src/debruijn/path_extend/extension_chooser.hpp | 581 +++++---
src/debruijn/path_extend/ideal_pair_info.hpp | 9 +-
src/debruijn/path_extend/loop_traverser.hpp | 10 +-
src/debruijn/path_extend/next_path_searcher.hpp | 103 +-
src/debruijn/path_extend/paired_library.hpp | 161 +--
src/debruijn/path_extend/path_extend_launch.hpp | 446 ++++--
src/debruijn/path_extend/path_extender.hpp | 673 +++++++---
src/debruijn/path_extend/pe_config_struct.cpp | 166 ++-
src/debruijn/path_extend/pe_config_struct.hpp | 97 +-
src/debruijn/path_extend/pe_io.hpp | 109 +-
src/debruijn/path_extend/pe_resolver.hpp | 198 ++-
src/debruijn/path_extend/pe_utils.hpp | 12 +-
.../scaffolder2015/connection_condition2015.cpp | 111 ++
.../scaffolder2015/connection_condition2015.hpp | 69 +
.../scaffolder2015/extension_chooser2015.cpp | 81 ++
.../scaffolder2015/extension_chooser2015.hpp | 49 +
.../scaffolder2015/scaff_supplementary.cpp | 66 +
.../scaffolder2015/scaff_supplementary.hpp | 75 ++
.../path_extend/scaffolder2015/scaffold_graph.cpp | 275 ++++
.../path_extend/scaffolder2015/scaffold_graph.hpp | 233 ++++
.../scaffolder2015/scaffold_graph_constructor.cpp | 73 +
.../scaffolder2015/scaffold_graph_constructor.hpp | 101 ++
.../scaffolder2015/scaffold_graph_visualizer.cpp | 71 +
.../scaffolder2015/scaffold_graph_visualizer.hpp | 73 +
src/debruijn/path_extend/split_graph_pair_info.hpp | 90 +-
src/debruijn/path_extend/weight_counter.hpp | 500 +++----
src/debruijn/path_utils.hpp | 15 +-
src/debruijn/positions.hpp | 2 +
src/debruijn/read_converter.hpp | 61 +-
src/debruijn/repeat.hpp | 371 -----
src/debruijn/repeat_resolving.cpp | 15 +-
src/debruijn/second_phase_setup.cpp | 5 +-
src/debruijn/sequence_mapper.hpp | 227 +++-
src/debruijn/sequence_mapper_notifier.hpp | 37 +-
src/debruijn/simplification.cpp | 399 +++++-
.../simplification/graph_simplification.hpp | 825 ++++++++++++
.../parallel_simplification_algorithms.hpp | 351 ++++-
.../simplification/simplification_settings.hpp | 212 +--
.../simplification/single_cell_simplification.hpp | 110 ++
src/debruijn/split_path_constructor.hpp | 19 +-
src/debruijn/stage.hpp | 8 +-
src/debruijn/stats/debruijn_stats.hpp | 243 ++--
.../contig_correctors/close_gaps_corrector.hpp | 4 +-
.../contig_correctors/overlap_searcher.hpp | 8 +-
.../contig_correctors/redundant_contig_remover.hpp | 8 +-
src/dipspades/dipspades.hpp | 14 +-
src/dipspades/dipspades_config.cpp | 2 +-
src/dipspades/dipspades_config.hpp | 2 +-
src/dipspades/main.cpp | 31 +-
.../bulge_paths_searcher.hpp | 9 +-
src/hammer/CMakeLists.txt | 2 +-
src/hammer/config_struct_hammer.cpp | 4 +-
src/hammer/config_struct_hammer.hpp | 2 +
src/hammer/expander.cpp | 14 +-
src/hammer/hamcluster.cpp | 86 +-
src/hammer/hamcluster.hpp | 9 +
src/hammer/hammer_tools.cpp | 4 +-
src/hammer/kmer_data.cpp | 265 +++-
src/hammer/main.cpp | 15 +-
src/hammer/misc/memusg | 2 +-
src/hammer/read_corrector.cpp | 45 +-
src/hammer/read_corrector.hpp | 7 +-
src/include/adt/concurrent_dsu.hpp | 314 +++--
src/include/adt/flat_map.hpp | 320 +++++
src/include/adt/flat_set.hpp | 230 ++++
src/include/adt/function_traits.hpp | 70 +
src/include/adt/iterator_range.hpp | 13 +
src/include/adt/queue_iterator.hpp | 14 +
src/include/adt/small_pod_vector.hpp | 379 ++++++
src/include/de/conj_iterator.hpp | 140 ++
src/include/de/data_divider.hpp | 2 +-
src/include/de/distance_estimation.hpp | 60 +-
src/include/de/extensive_distance_estimation.hpp | 69 +-
src/include/de/index_point.hpp | 455 +++++++
src/include/de/insert_size_refiner.hpp | 97 +-
src/include/de/pair_info_filters.hpp | 161 +--
src/include/de/paired_info.hpp | 1417 ++++++++++----------
src/include/de/paired_info_helpers.hpp | 149 ++
src/include/de/smoothing_distance_estimation.hpp | 33 +-
src/include/de/weighted_distance_estimation.hpp | 14 +-
src/include/func.hpp | 116 +-
src/include/graph_print_utils.hpp | 4 +-
src/include/io/kmer_iterator.hpp | 54 +
src/include/io/library.hpp | 48 +-
src/include/io/mmapped_reader.hpp | 68 +-
src/include/io/paired_read.hpp | 100 +-
src/include/io/read.hpp | 7 +-
src/{corrector => include/io/sam}/read.hpp | 101 +-
src/{corrector => include/io/sam}/sam_reader.hpp | 5 +-
src/include/io/single_read.hpp | 171 ++-
src/include/logger/logger.hpp | 1 +
src/include/mph_index/MurmurHash3.h | 38 -
src/include/mph_index/base_hash.hpp | 67 +-
src/include/mph_index/kmer_index.hpp | 10 +-
src/include/omni/action_handlers.hpp | 4 +-
src/include/omni/basic_edge_conditions.hpp | 42 +-
src/include/omni/bulge_remover.hpp | 784 ++++++++---
src/include/omni/complex_bulge_remover.hpp | 13 +-
src/include/omni/complex_tip_clipper.hpp | 8 +-
src/include/omni/coverage.hpp | 21 +-
.../omni/dijkstra_tools/dijkstra_algorithm.hpp | 354 ++---
.../omni/dijkstra_tools/dijkstra_helper.hpp | 50 +-
.../omni/dijkstra_tools/dijkstra_settings.hpp | 19 +-
.../omni/dijkstra_tools/vertex_process_checker.hpp | 55 +-
src/include/omni/edges_position_handler.hpp | 4 +
src/include/omni/erroneous_connection_remover.hpp | 73 +-
src/include/omni/graph_component.hpp | 6 +-
src/include/omni/graph_core.hpp | 27 +-
src/include/omni/graph_iterators.hpp | 107 +-
src/include/omni/graph_processing_algorithm.hpp | 88 +-
src/include/omni/mapping_path.hpp | 92 +-
src/include/omni/observable_graph.hpp | 72 +-
src/include/omni/omni_tools.hpp | 153 ++-
src/include/omni/order_and_law.hpp | 8 +-
src/include/omni/parallel_processing.hpp | 387 +++---
src/include/omni/path_processor.hpp | 418 +++---
src/include/omni/range.hpp | 92 ++
src/include/omni/relative_coverage_remover.hpp | 89 +-
src/include/omni/splitters.hpp | 10 +-
src/include/omni/tip_clipper.hpp | 78 +-
src/include/pred.hpp | 165 +++
src/include/sequence/rtseq.hpp | 6 +-
src/include/sequence/seq.hpp | 17 +-
src/include/sequence/simple_seq.hpp | 37 +-
src/include/simple_tools.hpp | 14 +
src/include/ssw/ssw.h | 138 +-
src/include/ssw/ssw_cpp.h | 50 +-
src/include/version.hpp.in | 7 +
src/io/CMakeLists.txt | 6 +-
src/io/library.cpp | 10 +-
src/io/sam/read.cpp | 42 +
src/{corrector => io/sam}/sam_reader.cpp | 20 +-
src/ionhammer/CMakeLists.txt | 2 +-
src/ionhammer/HSeq.hpp | 6 +-
src/ionhammer/main.cpp | 2 +
src/mph_index/MurmurHash3.cpp | 345 -----
src/scaffold_correction/scaffold_correction.hpp | 11 +-
.../__pycache__/corrector_logic.cpython-34.pyc | Bin 0 -> 2257 bytes
.../__pycache__/dipspades_logic.cpython-34.pyc | Bin 0 -> 9800 bytes
.../__pycache__/dipspades_logic.cpython-35.pyc | Bin 0 -> 9746 bytes
.../__pycache__/hammer_logic.cpython-33.pyc | Bin 0 -> 6876 bytes
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.../__pycache__/options_storage.cpython-33.pyc | Bin 0 -> 19269 bytes
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src/spades_pipeline/common/SeqIO.pyc | Bin 0 -> 7634 bytes
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.../common/__pycache__/sam_parser.cpython-33.pyc | Bin 0 -> 15134 bytes
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src/spades_pipeline/common/alignment.pyc | Bin 0 -> 3118 bytes
src/spades_pipeline/common/parallel_launcher.pyc | Bin 0 -> 4205 bytes
src/spades_pipeline/common/sam_parser.pyc | Bin 0 -> 11960 bytes
src/spades_pipeline/easy_align.py | 43 +
src/spades_pipeline/hammer_logic.py | 2 +
src/spades_pipeline/options_storage.py | 61 +-
src/spades_pipeline/run_contig_breaker.py | 53 +-
src/spades_pipeline/spades_logic.py | 10 +-
src/spades_pipeline/support.py | 56 +-
.../__pycache__/barcode_extraction.cpython-34.pyc | Bin 0 -> 5268 bytes
.../__pycache__/barcode_extraction.cpython-35.pyc | Bin 0 -> 5250 bytes
.../__pycache__/break_by_coverage.cpython-33.pyc | Bin 0 -> 9213 bytes
.../__pycache__/break_by_coverage.cpython-34.pyc | Bin 0 -> 6014 bytes
.../__pycache__/break_by_coverage.cpython-35.pyc | Bin 0 -> 5969 bytes
.../__pycache__/generate_quality.cpython-33.pyc | Bin 0 -> 3155 bytes
.../__pycache__/generate_quality.cpython-34.pyc | Bin 0 -> 2126 bytes
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.../__pycache__/launch_options.cpython-34.pyc | Bin 0 -> 4470 bytes
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.../moleculo_filter_contigs.cpython-33.pyc | Bin 0 -> 2792 bytes
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.../moleculo_postprocessing.cpython-33.pyc | Bin 0 -> 3213 bytes
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.../reference_construction.cpython-34.pyc | Bin 0 -> 7113 bytes
.../reference_construction.cpython-35.pyc | Bin 0 -> 7080 bytes
.../__pycache__/string_dist_utils.cpython-34.pyc | Bin 0 -> 1904 bytes
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.../truspades/barcode_extraction.py | 5 +-
.../truspades/barcode_extraction.pyc | Bin 0 -> 6460 bytes
src/spades_pipeline/truspades/break_by_coverage.py | 12 +-
.../truspades/break_by_coverage.pyc | Bin 0 -> 7561 bytes
src/spades_pipeline/truspades/generate_quality.pyc | Bin 0 -> 2396 bytes
src/spades_pipeline/truspades/id_generation.pyc | Bin 0 -> 3083 bytes
src/spades_pipeline/truspades/launch_options.py | 45 +-
src/spades_pipeline/truspades/launch_options.pyc | Bin 0 -> 5075 bytes
.../truspades/moleculo_filter_contigs.pyc | Bin 0 -> 2288 bytes
.../truspades/moleculo_postprocessing.pyc | Bin 0 -> 2568 bytes
.../truspades/reference_construction.pyc | Bin 0 -> 8701 bytes
.../truspades/string_dist_utils.pyc | Bin 0 -> 2474 bytes
truspades.py | 29 +-
truspades_manual.html | 15 +-
305 files changed, 17639 insertions(+), 8684 deletions(-)
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